TMEFF2

transmembrane protein with EGF like and two follistatin like domains 2

Basic information

Region (hg38): 2:191949043-192194933

Links

ENSG00000144339 ∙ NCBI:23671 ∙ OMIM:605734 ∙ HGNC:11867 ∙ Uniprot:Q9UIK5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TMEFF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEFF2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			8		1	9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	1

Variants in TMEFF2

This is a list of pathogenic ClinVar variants found in the TMEFF2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-191950393-C-A		not specified	Uncertain significance (Apr 01, 2024)
2-191953730-A-G		not specified	Uncertain significance (Dec 11, 2023)
2-191953740-C-T		not specified	Uncertain significance (Jan 10, 2022)
2-191953791-T-C		not specified	Uncertain significance (Nov 12, 2021)
2-191956313-C-T		not specified	Uncertain significance (Jun 29, 2023)
2-191998268-A-G		not specified	Uncertain significance (Aug 09, 2021)
2-192057773-G-A			Benign (Mar 29, 2018)
2-192184416-C-T		not specified	Uncertain significance (Jan 04, 2024)
2-192194398-T-C		not specified	Uncertain significance (May 17, 2023)
2-192194462-C-A		not specified	Uncertain significance (Jun 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEFF2	protein_coding	protein_coding	ENST00000272771	10	246667

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000739	0.996	125729	0	19	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.60	140	204	0.685	0.00000985	2465
Missense in Polyphen		40	65.206	0.61344		758
Synonymous	0.792	70	79.0	0.887	0.00000431	672
Loss of Function	2.54	11	24.6	0.447	0.00000129	274

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000143	0.000132
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be a survival factor for hippocampal and mesencephalic neurons. The shedded form up-regulates cancer cell proliferation, probably by promoting ERK1/2 phosphorylation. {ECO:0000269|PubMed:10903839, ECO:0000269|PubMed:17942404}.
• Pathway: Validated targets of C-MYC transcriptional repression (Consensus)

Recessive Scores

• pRec: 0.262

Intolerance Scores

• loftool: 0.420
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.29

Haploinsufficiency Scores

• pHI: 0.370
• hipred: Y
• hipred_score: 0.773
• ghis: 0.595

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Tmeff2
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype

Gene ontology

• Biological process: negative regulation of cell migration;wound healing, spreading of cells;negative regulation of integrin biosynthetic process;negative regulation of stress fiber assembly
• Cellular component: extracellular region;integral component of membrane
• Molecular function: molecular_function